#include "tree.h"
-
+/*****************************************************************/
+Tree::Tree(string g) {
+ try {
+ globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
+
+ parseTreeFile(); globaldata->runParse = false;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree - just parse");
+ exit(1);
+ }
+}
/*****************************************************************/
Tree::Tree() {
try {
globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; }
//for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; }
numNodes = 2*numLeaves - 1;
tree.resize(numNodes);
+
+ //initialize groupNodeInfo
+ for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
+ groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ }
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->Treenames[i]);
- tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+
+ //save group info
+ string group = globaldata->gTreemap->getGroup(globaldata->Treenames[i]);
+ vector<string> tempGroups; tempGroups.push_back(group);
+ tree[i].setGroup(tempGroups);
+ groupNodeInfo[group].push_back(i);
+
//set pcount and pGroup for groupname to 1.
- tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
- tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+ tree[i].pcount[group] = 1;
+ tree[i].pGroups[group] = 1;
+
//Treemap knows name, group and index to speed up search
globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
- tree[i].setGroup("");
+ vector<string> tempGroups;
+ tree[i].setGroup(tempGroups);
}
}
}
catch(exception& e) {
- errorOut(e, "Tree", "Tree");
+ m->errorOut(e, "Tree", "Tree");
exit(1);
}
}
/*****************************************************************/
Tree::~Tree() {}
/*****************************************************************/
+void Tree::addNamesToCounts() {
+ try {
+ //ex. seq1 seq2,seq3,se4
+ // seq1 = pasture
+ // seq2 = forest
+ // seq4 = pasture
+ // seq3 = ocean
+
+ //before this function seq1.pcount = pasture -> 1
+ //after seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
+
+ //before this function seq1.pgroups = pasture -> 1
+ //after seq1.pgroups = pasture -> 1 since that is the dominant group
+
+
+ //go through each leaf and update its pcounts and pgroups
+
+ //float A = clock();
+
+ for (int i = 0; i < numLeaves; i++) {
+
+ string name = tree[i].getName();
+
+ map<string, string>::iterator itNames = globaldata->names.find(name);
+
+ if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else {
+ vector<string> dupNames;
+ m->splitAtComma(globaldata->names[name], dupNames);
+
+ map<string, int>::iterator itCounts;
+ int maxPars = 1;
+ set<string> groupsAddedForThisNode;
+ for (int j = 0; j < dupNames.size(); j++) {
+
+ string group = globaldata->gTreemap->getGroup(dupNames[j]);
+
+ if (dupNames[j] != name) {//you already added yourself in the constructor
+
+ if (groupsAddedForThisNode.count(group) == 0) { groupNodeInfo[group].push_back(i); groupsAddedForThisNode.insert(group); } //if you have not already added this node for this group, then add it
+
+ //update pcounts
+ itCounts = tree[i].pcount.find(group);
+ if (itCounts == tree[i].pcount.end()) { //new group, add it
+ tree[i].pcount[group] = 1;
+ }else {
+ tree[i].pcount[group]++;
+ }
+
+ //update pgroups
+ itCounts = tree[i].pGroups.find(group);
+ if (itCounts == tree[i].pGroups.end()) { //new group, add it
+ tree[i].pGroups[group] = 1;
+ }else {
+ tree[i].pGroups[group]++;
+ }
+
+ //keep highest group
+ if(tree[i].pGroups[group] > maxPars){
+ maxPars = tree[i].pGroups[group];
+ }
+ }else { groupsAddedForThisNode.insert(group); } //add it so you don't add it to groupNodeInfo again
+ }//end for
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //update groups to reflect all the groups this node represents
+ vector<string> nodeGroups;
+ map<string, int>::iterator itGroups;
+ for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+ nodeGroups.push_back(itGroups->first);
+ }
+ tree[i].setGroup(nodeGroups);
+
+ }//end else
+ }//end for
+
+ //float B = clock();
+ //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "addNamesToCounts");
+ exit(1);
+ }
+}
+/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
//Treemap knows name, group and index to speed up search
}
catch(exception& e) {
- errorOut(e, "Tree", "getIndex");
+ m->errorOut(e, "Tree", "getIndex");
exit(1);
}
}
globaldata->gTreemap->setIndex(searchName, index);
}
catch(exception& e) {
- errorOut(e, "Tree", "setIndex");
+ m->errorOut(e, "Tree", "setIndex");
exit(1);
}
}
/*****************************************************************/
-void Tree::assembleTree() {
+int Tree::assembleTree() {
try {
+ //float A = clock();
+
+ //if user has given a names file we want to include that info in the pgroups and pcount info.
+ if(globaldata->names.size() != 0) { addNamesToCounts(); }
+
//build the pGroups in non leaf nodes to be used in the parsimony calcs.
for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
tree[i].pGroups = (mergeGroups(i));
tree[i].pcount = (mergeGcounts(i));
}
+ //float B = clock();
+ //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
+ return 0;
}
catch(exception& e) {
- errorOut(e, "Tree", "assembleTree");
+ m->errorOut(e, "Tree", "assembleTree");
exit(1);
}
}
+/*****************************************************************/
+int Tree::assembleTree(string n) {
+ try {
+
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ //float B = clock();
+ //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "assembleTree");
+ exit(1);
+ }
+}
+
/*****************************************************************/
void Tree::getCopy(Tree* copy) {
try {
//copy pcount
tree[i].pcount = copy->tree[i].pcount;
}
+
+ groupNodeInfo = copy->groupNodeInfo;
+
}
catch(exception& e) {
- errorOut(e, "Tree", "getCopy");
+ m->errorOut(e, "Tree", "getCopy");
exit(1);
}
}
return parsimony;
}
catch(exception& e) {
- errorOut(e, "Tree", "mergeGroups");
+ m->errorOut(e, "Tree", "mergeGroups");
exit(1);
}
}
//loop through nodes groups removing the ones the user doesn't want
for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
- if (inUsersGroups(it->first, g) != true) {
+ if (m->inUsersGroups(it->first, g) != true) {
tree[lc].pGroups.erase(it++);
}else { it++; }
}
//loop through nodes groups removing the ones the user doesn't want
for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
- if (inUsersGroups(it->first, g) != true) {
+ if (m->inUsersGroups(it->first, g) != true) {
tree[rc].pGroups.erase(it++);
}else { it++; }
}
return parsimony;
}
catch(exception& e) {
- errorOut(e, "Tree", "mergeUserGroups");
+ m->errorOut(e, "Tree", "mergeUserGroups");
exit(1);
}
}
return sum;
}
catch(exception& e) {
- errorOut(e, "Tree", "mergeGcounts");
+ m->errorOut(e, "Tree", "mergeGcounts");
exit(1);
}
}
void Tree::randomLabels(vector<string> g) {
try {
+
+ //initialize groupNodeInfo
+ for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
+ groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ }
for(int i = 0; i < numLeaves; i++){
int z;
//if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
bool treez, treei;
- treez = inUsersGroups(tree[z].getGroup(), g);
- treei = inUsersGroups(tree[i].getGroup(), g);
+ treez = m->inUsersGroups(tree[z].getGroup(), g);
+ treei = m->inUsersGroups(tree[i].getGroup(), g);
if ((treez == true) && (treei == true)) {
//switches node i and node z's info.
tree[z].pGroups = (tree[i].pGroups);
tree[i].pGroups = (lib_hold);
- string zgroup = tree[z].getGroup();
+ vector<string> zgroup = tree[z].getGroup();
tree[z].setGroup(tree[i].getGroup());
tree[i].setGroup(zgroup);
tree[z].pcount = (tree[i].pcount);
tree[i].pcount = (gcount_hold);
}
+
+ for (int k = 0; k < (tree[i].getGroup()).size(); k++) { groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
+ for (int k = 0; k < (tree[z].getGroup()).size(); k++) { groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
}
}
catch(exception& e) {
- errorOut(e, "Tree", "randomLabels");
+ m->errorOut(e, "Tree", "randomLabels");
exit(1);
}
}
-/**************************************************************************************************/
+/**************************************************************************************************
void Tree::randomLabels(string groupA, string groupB) {
try {
}
}
catch(exception& e) {
- errorOut(e, "Tree", "randomLabels");
+ m->errorOut(e, "Tree", "randomLabels");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Tree", "randomBlengths");
+ m->errorOut(e, "Tree", "randomBlengths");
exit(1);
}
}
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(vector<string> g) {
randomLabels(g);
- assembleTree();
+ assembleTree("noNameCounts");
}
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
- randomLabels(groupA, groupB);
- assembleTree();
+
+ vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+ randomLabels(temp);
+ assembleTree("noNameCounts");
}
/*************************************************************************************************/
}
}
catch(exception& e) {
- errorOut(e, "Tree", "randomTopology");
+ m->errorOut(e, "Tree", "randomTopology");
exit(1);
}
}
out << ";" << endl;
}
catch(exception& e) {
- errorOut(e, "Tree", "print");
+ m->errorOut(e, "Tree", "print");
exit(1);
}
}
out << ";" << endl;
}
catch(exception& e) {
- errorOut(e, "Tree", "printForBoot");
+ m->errorOut(e, "Tree", "printForBoot");
exit(1);
}
}
void Tree::createNewickFile(string f) {
try {
int root = findRoot();
- //filename = getRootName(globaldata->getTreeFile()) + "newick";
+ //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
filename = f;
- openOutputFile(filename, out);
+ m->openOutputFile(filename, out);
printBranch(root, out, "branch");
out.close();
}
catch(exception& e) {
- errorOut(e, "Tree", "createNewickFile");
+ m->errorOut(e, "Tree", "createNewickFile");
exit(1);
}
}
return -1;
}
catch(exception& e) {
- errorOut(e, "Tree", "findRoot");
+ m->errorOut(e, "Tree", "findRoot");
exit(1);
}
}
}
}
}else { //you are a leaf
- out << tree[node].getGroup();
+ string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+
+ out << leafGroup;
if (mode == "branch") {
//if there is a branch length then print it
if (tree[node].getBranchLength() != -1) {
}
catch(exception& e) {
- errorOut(e, "Tree", "printBranch");
+ m->errorOut(e, "Tree", "printBranch");
exit(1);
}
}
try {
string filename = globaldata->getTreeFile();
ifstream filehandle;
- openInputFile(filename, filehandle);
+ m->openInputFile(filename, filehandle);
int c, comment;
comment = 0;
int done = 1;
}
}
filehandle.close();
+
+ //for (int i = 0; i < globaldata->Treenames.size(); i++) {
+//cout << globaldata->Treenames[i] << endl; }
+//cout << globaldata->Treenames.size() << endl;
}
catch(exception& e) {
- errorOut(e, "Tree", "parseTreeFile");
+ m->errorOut(e, "Tree", "parseTreeFile");
exit(1);
}
}
return 0;
}
catch(exception& e) {
- errorOut(e, "Tree", "readTreeString");
+ m->errorOut(e, "Tree", "readTreeString");
exit(1);
}
}
projects / mothur.git / blobdiff